Would it be a kindness to try and capture Peter and reunite him with his girl friend?
Short Answer: No
Long complex answer:
Rabbit bonding has several considerations, we have several posts here. The short version is that separating bonded bunnies can cause them to die of loneliness. The highest risk is in the first few days. Your question indicates that it has been several months. While they can see each other, they are not able to interact. I believe you are past this hurdle. Neither is going to die of loneliness without the other.
You don't say if your female rabbit is spayed. I will assume she is not. Most importantly, in the US, wild rabbits and domestic rabbits can not make babies. But the hormones they make can affect each other. If you have female rabbits that are not spayed, the hormones are probably what is causing the male wild rabbit to visit. Getting the females spayed should sharply decrease his visits. It can take up to a month before the existing hormones are gone.
Caging any rabbit for the long term is probably not a kindness. Rabbits live 8 to 12 years and need a lot of room. Personally I think at least a bedroom size area. Rabbits are easy to toilet train so moving her into your bedroom could be the best choice.
Outdoor rabbits, particularly those who interact with or are in the same area as wild rabbits, can get [diseases and parasites].(Can domestic rabbits carry diseases if left outdoors for too long then brought in?) You will probably want to contact your vet about treatment options. Use care in choosing a treatment as some can be fatal to rabbits.
Lastly there are a number of issues with making a wild rabbit into a pet. They are addressed in Can I make a baby wild rabbit a pet?
TL:DR The kindest thing would be to get your female rabbit spayed, move her into your bedroom, and leave Peter outside.